This tool was developed to facilitate the design of artificial microRNAs (amiRNAs) in plants.
Once you have selected a mature 21-nt miRNA for your target sequence, you must paste it into the software platform. The program will return the resulting designed oligomers to built the pre-amiRNA molecule.
Aditionally, the program also will offer you a pair of primers to perform a second PCR step which add "attB-B" recombination sites required for Gateway cloning technology.
For evaluation purposes, you be able to detect mature amiRNA using Stem-loop pulsed RT-PCR. The software provides you also a specific RT-primer and two end-point PCR primers needed to carry out the stem-loop PCR.
Notice that amiRNA generated by the system could be different from user input miRNA sequence. If you need to detect the endogenous miRNA or any other small RNA molecule (15-40 nt) by Stem-loop pulsed RT-PCR you must use the 'Stem-loop primers Designer' tool.